Biweekly release (22-05-05)

.eslintrc.js

@@ -25,6 +25,7 @@ module.exports = {
   },
   env: {
     browser: true,
+    node: true,
     es6: true,
   },
   settings: {

CHANGELOG.md

@@ -1,5 +1,21 @@
 # Changelog
 
+## 2022-05-05
+
+### New features
+
+- Added export to BibTex for each paper (frontend interface & backend endpoint).
+- Added BASE document type tags with icons.
+- New share buttons.
+
+### Changes
+
+- New look and feel (design & CSS changes).
+
+### Security
+
+- Periodical npm security update.
+
 ## 2022-03-28
 
 ### Changes

examples/project_website/base.html

@@ -87,9 +87,11 @@
     <script>
         data_config.files = [{
             //title: "digital education",
-            title: "calcium",
+            //title: "calcium",
+            title: "production",
             //file: "./data/digital-education.json"
-            file: "./data/calcium.json"
+            //file: "./data/calcium.json",
+            file: "./data/production.json"
         }]
         data_config.server_url = window.location.href.replace(/[^/]*$/, '') + "./headstart/server/";
     </script>

examples/project_website/css/main.css

@@ -2591,15 +2591,6 @@ time {
     margin-bottom: 0px;
 }
 
-.citation {
-    display: inline-block;
-    padding: 10px;
-    background-color: rgba(239,243,244,1);
-    hyphens: none;
-    border-radius: 3px;
-    -moz-border-radius: 3px;
-}
-
 .overflow-vis {
     overflow-y: hidden;
 }

examples/project_website/data-config_base.js

@@ -28,7 +28,7 @@ var data_config = {
   context_most_relevant_tooltip: true,
 
   embed_modal: true,
-  share_modal: true,
+  share_modal: false,
 
   doi_outlink: true,
   filter_menu_dropdown: true,
@@ -46,4 +46,7 @@ var data_config = {
 
   highlight_query_terms: true,
   show_context_oa_number: false,
+
+  show_twitter_button: true,
+  show_email_button: true,
 };

package.json

@@ -7,7 +7,7 @@
     "doc": "doc"
   },
   "scripts": {
-    "test": "jest",
+    "test": "TZ='Europe/Vienna' jest",
     "dev": "webpack --progress --watch --mode=development",
     "prod": "webpack --progress",
     "start": "webpack serve --progress --mode=development --env publicPath=http://localhost:8080/dist/",

server/preprocessing/other-scripts/utils.R

@@ -110,6 +110,9 @@ detect_error <- function(failed, service) {
       if (grepl("xml_find_first", failed$query_reason, fixed=TRUE)){
         reason <- c(reason, 'API error: BASE not reachable')
       }
+      if (grepl("read_xml.raw", failed$query_reason, fixed=TRUE)){
+        reason <- c(reason, 'API error: BASE not reachable')
+      }
     }
     if (length(reason) == 0 && service == 'pubmed') {
       if (startsWith(failed$query_reason, "HTTP failure: 500") && grepl("error forwarding request", failed$query_reason, fixed=TRUE)){

server/services/exportMetadata.php

@@ -0,0 +1,44 @@
+<?php
+
+require_once dirname(__FILE__) . '/../classes/headstart/library/CommUtils.php';
+require_once dirname(__FILE__) . '/../classes/headstart/library/APIClient.php';
+require_once dirname(__FILE__) . '/../classes/headstart/library/toolkit.php';
+use headstart\library;
+
+function export($export_format, $metadata_json) {
+    $INI_DIR = dirname(__FILE__) . "/../preprocessing/conf/";
+    $ini_array = library\Toolkit::loadIni($INI_DIR);
+    $apiclient = new \headstart\library\APIClient($ini_array);
+
+
+    $payload = $metadata_json;
+    #$res = $apiclient->call_persistence("export/" . $export_format, $payload);
+    $res = $apiclient->call_api("export/" . $export_format, $payload);
+    return $res;
+};
+
+$json = $_POST['paper'];
+$format = (isset($_REQUEST['format'])) ? $_REQUEST['format'] : "bibtex";
+$download = (isset($_REQUEST['download'])) ? $_REQUEST['download'] : false;
+$result = export($format, $json);
+
+if (isset($result["status"]) && $result["status"] === "error") {
+    header('Content-type: application/json');
+    echo json_encode($result);
+}
+
+if ($format == "bibtex") {
+    $format = "bib";
+}
+
+if (isset($download) & $download==true ) {
+    header('Content-type: application/text');
+    header('Content-Disposition: attachment; filename=metadata.' . $format);
+} else {
+    header('Content-type: text/plain');
+}
+
+$result = json_decode($result["result"], true);
+echo $result["export"];
+
+?>

server/workers/api/requirements.txt

@@ -12,3 +12,4 @@ pandas
 pyyaml
 flasgger
 psycopg2-binary
+bibtexparser